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metanetwork (version 0.7.0)

Handling and Representing Trophic Networks in Space and Time

Description

A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks.

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Install

install.packages('metanetwork')

Monthly Downloads

218

Version

0.7.0

License

GPL-3

Issues

3

Pull Requests

0

Stars

2

Forks

1

Maintainer

Marc Ohlmann

Last Published

December 5th, 2022

Functions in metanetwork (0.7.0)

print

print metanetwork
is.metanetwork

Test of belonging to class metanetwork
meta_angola

Angola fishery metanetwork metanetwork built from: Angelini & Velho 2011, Data from: Angelini, R., Velho, VF. (2011) Ecosystem structure and trophic analysis of Angolan fishery landings. Scientia Marina 75(2)
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Pipe
visNetwork.default

Default configuration for visNetwork
meta_norway

Norway soil metanetwork metanetwork built from: Calderon-Sanou et al. 2021, Data from: Calderon-Sanou, I., Munkemuller, T., Zinger, L., Schimann, H., Yoccoz, N. G., Gielly, L., ... & Thuiller, W. (2021). Cascading effects of moth outbreaks on subarctic soil food webs. Scientific reports, 11(1), 1-12.
meta_vrtb

European vertebrates metanetwork metanetwork built using data from: O'Connor, L. M., Pollock, L. J., Braga, J., Ficetola, G. F., Maiorano, L., Martinez-Almoyna, C., ... & Thuiller, W. (2020). Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche. Journal of Biogeography, 47(1), 181-192. and Maiorano, L., Montemaggiori, A., Ficetola, G. F., O'connor, L., & Thuiller, W. (2020). TETRA-EU 1.0: a species-level trophic metaweb of European tetrapods. Global Ecology and Biogeography, 29(9), 1452-1457.
vismetaNetwork

vismetaNetwork
ggnet.default

Default configuration for ggnet
ggmetanet

ggmetanet
append_agg_nets

append aggregated networks
attach_layout

compute and attach metanetwork layouts
extract_networks

extract networks from a metanetwork object
compute_TL

compute trophic levels
build_metanet

Build metanetwork object
diff_plot

plot difference network
TL_tsne.default

Default configuration for the diffusion kernel based t-sne
group_layout.default

Default configuration for group-TL-tsne layout
metanet_pipe

Execute 'metanetwork' pipeline
metanet_build_pipe

Build and execute 'metanetwork' pipeline
plot_trophicTable

Plot trophic groups hierarchy